Contacts of the strand formed by residues 188 - 197 (chain B) in PDB entry 2F1X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 188 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 3.9 22.0 - - + -
75B VAL 3.5 4.5 - - - -
76B GLU* 2.5 42.3 + - + +
143B TYR* 2.8 24.9 + - + +
183B PHE 3.7 0.5 - - - +
185B ASP* 3.0 30.8 + - - +
186B ASP* 3.7 26.1 + - + +
187B ASP* 1.3 82.6 - - - +
189B VAL* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 4.5 0.4 - - - -
75B VAL 3.0 28.2 + - - +
78B PHE* 3.4 44.6 - - + -
140B ILE* 3.6 28.7 - - + -
143B TYR* 3.7 0.4 - - - -
176B VAL* 3.9 13.0 - - + -
183B PHE 3.7 11.7 - - - +
184B ILE* 3.9 17.7 - - + -
188B LYS* 1.3 77.7 - - - +
190B THR* 1.3 62.7 + - - +
191B PHE* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 4.1 18.2 - - + +
73B PHE 3.7 4.0 - - - +
74B THR* 2.6 29.0 + - - +
140B ILE* 3.6 3.9 - - - +
141B ILE* 3.0 57.8 + - + +
143B TYR* 3.4 27.0 + - - -
183B PHE 4.6 0.6 + - - -
189B VAL* 1.3 73.2 - - - +
191B PHE* 1.3 71.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN* 3.3 5.9 - - - +
73B PHE* 3.0 39.6 + + - +
75B VAL* 3.9 18.2 - - + -
78B PHE* 3.6 21.1 - + - -
99B ILE* 3.6 12.4 - - + +
101B VAL* 3.6 36.8 - - + -
115B VAL* 4.0 9.6 - - + -
117B PHE* 3.7 28.9 - + + -
139B LYS 3.6 2.9 - - - -
140B ILE* 3.4 36.8 - - + -
189B VAL* 3.6 22.9 - - + -
190B THR* 1.3 75.6 - - - +
192B GLU* 1.3 60.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.6 30.1 - - + +
71B PHE 3.5 7.4 - - - +
72B GLN* 3.7 20.7 + - + +
117B PHE* 3.6 1.7 - - - -
137B VAL 3.6 0.7 - - - +
139B LYS* 2.7 76.2 + - + +
141B ILE* 4.3 11.2 - - + +
191B PHE* 1.3 74.4 - - - +
193B VAL* 1.3 74.9 + - - +
194B PHE* 5.4 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA 3.4 1.9 - - - +
70B THR* 3.1 8.3 - - - -
71B PHE* 3.0 53.3 + - + -
99B ILE* 3.5 25.4 - - + -
117B PHE* 4.0 13.0 - - + -
119B LEU* 4.0 19.7 - - + -
136B ALA* 4.5 2.7 - - + -
137B VAL 3.4 4.9 - - - +
138B LEU* 4.3 11.0 - - + -
192B GLU* 1.3 81.9 - - - +
194B PHE* 1.3 71.6 + - - +
195B VAL* 3.9 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU* 3.5 37.7 - - + -
69B ALA* 3.5 7.9 - - - -
70B THR* 3.4 22.7 - - + +
135B GLN 4.0 0.2 - - - +
136B ALA* 3.0 5.1 - - - +
137B VAL* 2.8 57.2 + - + -
192B GLU* 5.1 4.2 + - - +
193B VAL* 1.3 72.5 - - - +
195B VAL* 1.3 60.1 + - - +
196B GLN* 3.6 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER 3.9 0.9 - - - +
68B GLU* 3.1 3.6 - - - -
69B ALA 3.0 36.5 + - - +
71B PHE* 4.4 10.1 - - + -
92B VAL* 4.2 19.4 - - + +
97B TRP* 4.0 28.9 - - + -
119B LEU* 4.0 7.6 - - + -
134B ALA* 3.9 20.2 - - + -
135B GLN 3.5 8.5 - - - +
136B ALA* 3.8 7.4 - - + -
193B VAL* 4.0 15.3 - - + -
194B PHE* 1.3 75.4 - - - +
196B GLN* 1.3 68.2 + - - +
197B ALA* 4.5 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.4 5.8 - - - +
68B GLU* 2.9 37.2 + - + +
133B HIS 4.1 0.5 - - - +
134B ALA* 3.2 4.2 - - - -
135B GLN* 2.9 62.9 + - - +
194B PHE* 3.6 28.3 - - + -
195B VAL* 1.3 71.8 - - - +
197B ALA* 1.3 60.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 2.8 15.9 + - - +
92B VAL* 4.6 3.8 - - + -
93B ARG* 2.8 44.7 + - + -
97B TRP* 3.7 29.4 - - + -
132B CYS* 4.6 6.1 - - + -
133B HIS 3.6 4.9 - - - +
134B ALA* 3.9 4.5 - - + -
195B VAL* 4.1 1.4 + - + -
196B GLN* 1.3 74.6 - - - +
198B ASP* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il